AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00290_bbur_reg_100.orf -o00290_bbur_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Purged sequences:
BB0736	51	B. burgdorferi predicted coding region BB0736

Input sequences:
#1	BB0251	202	leucyl-tRNA synthetase (leuS)
#2	BB0735	66	rare lipoprotein A (rlpA)
#3	BB0834	22	ATP-dependent Clp protease, subunit C (clpC)
#4	BB0835	114	phosphomannomutase (cpsG)

Motif number 1

AATTGTTAGCAAATTATTAAATAAAATTAAC	1	119	1	AAATTATTAA	    0.965168	-84
TTATTAAATAAAATTAACAAAAATGCAATCT	1	132	1	AAATTAACAA	    0.949099	-71
ACAAAAATGCAATCTAAAAGAATATTAGAGA	1	148	1	AATCTAAAAA	    0.851126	-55
GTCCTCTTGAAAATTAACTCATAACAACTTA	1	180	0	AAATTAACTA	    0.806866	-23
TTTTATAATTAAATCAAAAAAAATGTAAATA	2	28	1	AAATCAAAAA	    0.856862	-39
CATAACAGAAAATTTAATAAAT         	3	11	1	AATTTAATAA	    0.986584	-12
          AATTTAATACACATTCTTATA	4	1	1	AATTTAATAA	    0.986586	-114
ATTATCATATAATTTATAAGAATGTGTATTA	4	15	0	AATTTATAAA	    0.960304	-100
CTTGATATAGAATTTATTATCATATAATTTA	4	30	0	AATTTATTAC	    0.901687	-85
TCAAGTATATAATTCATTATAAATCAATATA	4	56	1	AATTCATTAA	     0.94876	-59
AAATCAATATAATTTAATTAATCTTTGTTTA	4	76	1	AATTTAATTA	    0.942788	-39
ATTTCCTTTTATTTTATTAAACAAAGATTAA	4	93	0	ATTTTATTAA	    0.860883	-22
          ********* *

Masking position 6
Map Score:   16.6427

Number of sites scoring better than the average of aligned sites = 1334
Number in coding regions = 835
Number in noncoding regions = 499
Number of orfs with sites within 600 bp upstream = 120
Fraction of orfs with sites within 600 bp upstream = 0.019274


Motif number 2

          AAAATATAATGGTTAATAGT	1	1	1	AAAATATAAT	     0.94577	-202
AGCAAATTATTAAATAAAATTAACAAAAAT	1	126	1	TAAATAAAAT	    0.881598	-77
AAAATTAACAAAAATGCAATCTAAAAGAAT	1	141	1	AAAATGCAAT	    0.885575	-62
AATGCAATCTAAAAGAATATTAGAGAATAA	1	153	1	AAAAGAATAT	    0.721356	-50
TGTCCTCTTGAAAATTAACTCATAACAACT	1	182	0	AAAATTAACT	     0.73918	-21
TTTAATTATAAAAAGAAAAAAGTCTAAAAA	2	11	0	AAAAGAAAAA	    0.831582	-56
TTTTCTTTTTATAATTAAATCAAAAAAAAT	2	22	1	ATAATTAAAT	    0.911083	-45
TAAATCAAAAAAAATGTAAATAAGCAATTT	2	37	1	AAAATGTAAA	    0.763242	-30
       CATAACAGAAAATTTAATAAAT 	3	4	1	AACAGAAAAT	    0.884227	-19
AGAATTTATTATCATATAATTTATAAGAAT	4	23	0	ATCATATAAT	    0.747999	-92
ATATTGATTTATAATGAATTATATACTTGA	4	56	0	ATAATGAATT	    0.692523	-59
ATAAATCAATATAATTTAATTAATCTTTGT	4	74	1	ATAATTTAAT	    0.825274	-41
TAATCTTTGTTTAATAAAATAAAAGGAAAT	4	94	1	TTAATAAAAT	    0.809336	-21
TTAATAAAATAAAAGGAAATA         	4	104	1	AAAAGGAAAT	    0.960949	-11
          **********

Masking position 4
Map Score:   12.1699

Number of sites scoring better than the average of aligned sites = 3500
Number in coding regions = 2301
Number in noncoding regions = 1199
Number of orfs with sites within 600 bp upstream = 217
Fraction of orfs with sites within 600 bp upstream = 0.0348538


Motif number 3

TCTACCACTTCCACCACCACAGCACTATTA	1	24	0	CCACCACCAC	    0.990495	-179
GGGCTTGCGCCCACTAGCCCCTCAAGCTAG	1	58	0	CCACTAGCCC	     0.99275	-145
GGGCTAGTGGGCGCAAGCCCGTGCTGGTTC	1	68	1	GCGCAAGCCC	    0.957396	-135
AACTGGACTTGAACCAGCACGGGCTTGCGC	1	78	0	GAACCAGCAC	    0.984441	-125
          **********

Masking position 6
Map Score:   1.05038

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 16
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

          **********

No masking
Map Score:   -1.60993e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -1.60993e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -1.60993e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0